Molecular detverection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains

Validation of a real-time PCR panel for detection and quantification of nine pathogens commonly associated with canine infectious respiratory disease

Canine infectious respiratory disease (CIRD) is a complicated respiratory syndrome in dogs [1], [2], [3]. A panel PCR was developed [4] to detect nine pathogens commonly associated with CIRD: Mycoplasma cynos, Mycoplasma canis, Bordetella bronchiseptica; canine adenovirus type 2, canine herpesvirus 1, canine parainfluenza virus, canine distemper virus, canine influenza virus and canine respiratory coronavirus [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16]. To evaluate diagnostic performance of the assay, 740 nasal swab and lung tissue samples were collected and tested with the new assay, and compared to an older version of the assay detecting the same pathogens except that it does not differentiate the two Mycoplasma species. Results indicated that the new assay had the same level of specificity, but with higher diagnostic sensitivity and had identified additional samples with potential co-infections. To confirm the new assay is detecting the correct pathogens, samples with discrepant results between the two assays were sequence-confirmed. Spiking a high concertation target to samples carrying lower concentrations of other targets was carried out and the results demonstrated that there was no apparent interference among targets in the same PCR reaction. Another spike-in experiment was used to determine detection sensitivity between nasal swab and lung tissue samples, and similar results were obtained.•A nine-pathogen CIRD PCR panel assay had identified 139 positives from 740 clinical samples with 60 co-infections;•High-concentration target does not have apparent effect on detecting low-concentration targets;•Detection sensitivity were similar between nasal swab and lung tissue samples.

Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing

Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-time reverse transcriptase PCR assays targeting S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, and M:D3N. Using the combination of results for each of these markers, samples could be designated as belonging to sublineages within BA.1, BA.2, BA.4, or BA.5. The analytical sensitivity of these markers ranged from 132 to 2229 copies/mL and in-laboratory accuracy was 98.9-100%. A 97.3% agreement using 12,592 specimens was demonstrated for the assays compared to genome sequencing. The use of these assays, combined with genome sequencing, facilitated the surveillance of SARS-CoV-2 lineages throughout a BA.5-dominated period.

The coming Omicron waves and factors affecting its spread after China reopening borders

The Chinese government relaxed the Zero-COVID policy on Dec 15, 2022, and reopened the border on Jan 8, 2023. Therefore, COVID prevention in China is facing new challenges. Though there are plenty of prior studies on COVID, none is regarding the predictions on daily confirmed cases, and medical resources needs after China reopens its borders. To fill this gap, this study innovates a combination of the Erdos Renyl network, modified computational model [Formula: see text], and python code instead of only mathematical formulas or computer simulations in the previous studies. The research background in this study is Shanghai, a representative city in China. Therefore, the results in this study also demonstrate the situation in other regions of China. According to the population distribution and migration characteristics, we divided Shanghai into six epidemic research areas. We built a COVID spread model of the Erodos Renyl network. And then, we use python code to simulate COVID spread based on modified [Formula: see text] model. The results demonstrate that the second and third waves will occur in July-September and Oct-Dec, respectively. At the peak of the epidemic in 2023, the daily confirmed cases will be 340,000, and the cumulative death will be about 31,500. Moreover, 74,000 hospital beds and 3,700 Intensive Care Unit (ICU) beds will be occupied in Shanghai. Therefore, Shanghai faces a shortage of medical resources. In this simulation, daily confirmed cases predictions significantly rely on transmission, migration, and waning immunity rate. The study builds a mixed-effect model to verify further the three parameters' effect on the new confirmed cases. The results demonstrate that migration and waning immunity rates are two significant parameters in COVID spread and daily confirmed cases. This study offers theoretical evidence for the government to prevent COVID after China opened its borders.

Passive Surveillance of SARS-CoV-2 in Adult Blacklegged Ticks (Ixodes scapularis) from Northeast Pennsylvania

Monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wildlife is vital to public health. White-tailed deer (Odocoileus virginianus) in the United States have tested positive for SARS-CoV-2, and their interactions with blacklegged ticks (Ixodes scapularis) raise the question of whether or not these ticks also carry SARS-CoV-2. In this study, 449 blacklegged ticks from Northeast Pennsylvania were collected in the fall of 2022 and tested via RT-qPCR for the presence of SARS-CoV-2. Fourteen ticks were amplified with late quantification cycles (Cq) using primers from two nucleocapsid genes (N1 and N2) via TaqMan assays. Three of these samples were amplified on a SYBR green assay during secondary testing. However, melt curve and gel electrophoresis analysis verified negative results for these three samples. Genetic sequencing was performed on one of the three samples to look for potential cross-reactions causing the amplification observed. However, no significant match was found in the NCBI database. Although all 449 blacklegged ticks were negative for SARS-CoV-2, I. scapularis should continue to be tested for COVID-19. If blacklegged ticks test positive for COVID-19 in the future, research should focus on determining the stability of SARS-CoV-2 with the tick vector and the potential for transmission through tick bites.

Visualized Lateral Flow Assay for Dual Viral RNA Fragment Detection

In this technical note, we report an easy-to-produce, reverse-transcription-free, and protein-enzyme-free lateral flow assay for detection of viral RNA fragments by taking SARS-CoV-2 ORF1ab and N as target models. Catalytic hairpin assembly is utilized for dual RNA fragment orthogonal reaction to generate copious amounts of opened hairpin duplexes, which bridge DNA-modified gold nanoparticles and capture strands on the strip to induce coloration. The dual RNA fragments are simultaneously visualized during one time of sample flow, and single-base-mismatched nontarget sequences can be differentiated. The test strip can be flexibly adapted to detect evolutional SARS-CoV-2 variants such as Delta and Omicron. It also shows potential in visually detecting long-sequence virus simulants and achieves a sensitivity comparable to that of RT-qPCR by incorporation with upstream sample amplification. The lateral flow assay should offer a convenient and reliable technique for viral nucleic acid detection.

Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2

The emergence of mutations in the coronavirus genome provides opportunities for occurrence new strains with higher transmissibility, severity and duration of the disease poses. In 2020, a new variant of the coronavirus SARS-COV-2 - Delta was identified in India. This genetic variant has spread rapidly and became dominant in many countries, including Russia. In November 2021, a new outbreak of COVID-19 occurred in Africa driven by a variant SARS-COV-2 named later Omicron. Both variants had increased transmissibility compared to previously encountered variants and quickly, replacing its around the world. To promptly monitor the epidemiological situation in the country, to assess the spread of dominant genetic variants of the virus and to take appropriate measures, we have developed an RT‒PCR reagent kit for the identification of Delta and Omicron by detecting a corresponding combination of major mutations. The minimum set of mutations was chosen which allows to differentiate Delta and Omicron variants, in order to increase the analysis productivity and reduce costs. Primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Delta and Omicron. Similar approach can be implemented for the rapid development of assays for differentiating important SARS-COV-2 variants or for other viruses genotyping for epidemiological surveillance or for diagnostic use in order to assist in making clinical decisions. It was demonstrated that the results of VOC Delta and Omicron detection and their typical mutations were concordant with genotyping based on WGS results for all 847 samples of SARS-CoV-2 RNA. The kit has high analytical sensitivity (1х10³ copies/mL of SARS-CoV-2 RNA) for each of the detected genetic variants and possesses 100% analytic specificity for microorganism panel testing. The diagnostic sensitivity (95% confidence interval) obtained during pivotal trials was 91.1-100% for Omicron and 91.3-100% for Delta, while the diagnostic specificity with a 95% confidence interval was 92.2-100%. The use of a set of reagents in combination with sequencing of SARS-CoV-2 RNA as part of epidemiological monitoring made it possible to quickly track the dynamics of changes in Delta and Omicron prevalence in the Moscow region in the period from December 2021 to July 2022.

Assessment of the Risk and Symptoms of SARS-CoV-2 Infection Among Healthcare Workers During the Omicron Transmission Period: A Multicentric Study from Four Hospitals of Mainland China

Purpose

The SARS-CoV-2 omicron variant emerged and spread rapidly among the population in the early stage of China's normalized prevention and control in December 2022. Healthcare workers (HCWs) are particularly exposed to SARS-CoV-2, it is important to evaluate the impact of the omicron pandemic on HCWs in China.

Methods

A self-administered online survey was conducted on infected HCWs from four hospitals of Taizhou. A total of 748 HCWs received the survey via DingTalk, and 328 responded to the questionnaire. The risk factors were investigated using univariate and multivariate logistic regression analysis.

Results

By December 20, 2022, 748 HCWs tested positive by PCR, and the infection rate was 11.4% (748/6581). Among 328 respondents, the most common symptoms were cough (88.4%), fever (83.5%), runny nose (77.1%), sore throat (73.2%), headache (70.1%), muscle aches (67.1%), and fatigue (53.4%). 69.8% (229/328) of the participants had five or more major onset symptoms, while no severe case was observed. The multivariate analysis indicated that the poor sleep quality (OR = 2.29, 95% CI: 1.31-4.02, P = 0.004) was an independent risk factor for more major onset symptoms, while wore gloves ≥95% times in working (OR = 0.49, 95% CI: 0.28-0.85, P = 0.011) was significantly related to fewer symptoms. In addition, 239 (72.9%) recipients reported high fever (temperature ≥38.5°C), less common cold (≤3 vs >3 times/year, OR = 2.20, 95% CI: 1.05-4.65, P = 0.038) was significantly associated with high fever.

Conclusion

Our findings imply rapid transmissibility of omicron and multiple-onset symptoms among HCWs. Improved autoimmunity and self-protection measures for HCWs may be helpful in controlling infection and clinical symptoms. Our results provide empirical reference values for improved countermeasures and protective measures for major public health emergencies.

Machine Learning-Assisted Real-Time Polymerase Chain Reaction and High-Resolution Melt Analysis for SARS-CoV-2 Variant Identification

Since the declaration of COVID-19 as a pandemic in early 2020, multiple variants of the severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) have been detected. The emergence of multiple variants has raised concerns due to their impact on public health. Therefore, it is crucial to distinguish between different viral variants. Here, we developed a machine learning web-based application for SARS-CoV-2 variant identification via duplex real-time polymerase chain reaction (PCR) coupled with high-resolution melt (qPCR-HRM) analysis. As a proof-of-concept, we investigated the platform's ability to identify the Alpha, Delta, and wild-type strains using two sets of primers. The duplex qPCR-HRM could identify the two variants reliably in as low as 100 copies/μL. Finally, the platform was validated with 167 nasopharyngeal swab samples, which gave a sensitivity of 95.2%. This work demonstrates the potential for use as automated, cost-effective, and large-scale viral variant surveillance.

Current strategies for SARS-CoV-2 molecular detection

The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.

An Update on Detection Technologies for SARS-CoV-2 Variants of Concern

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the global epidemic of Coronavirus Disease 2019 (COVID-19), with a significant impact on the global economy and human safety. Reverse transcription-quantitative polymerase chain reaction (RT-PCR) is the gold standard for detecting SARS-CoV-2, but because the virus's genome is prone to mutations, the effectiveness of vaccines and the sensitivity of detection methods are declining. Variants of concern (VOCs) include Alpha, Beta, Gamma, Delta, and Omicron, which are able to evade recognition by host immune mechanisms leading to increased transmissibility, morbidity, and mortality of COVID-19. A range of research has been reported on detection techniques for VOCs, which is beneficial to prevent the rapid spread of the epidemic, improve the effectiveness of public health and social measures, and reduce the harm to human health and safety. However, a meaningful translation of this that reduces the burden of disease, and delivers a clear and cohesive message to guide daily clinical practice, remains preliminary. Herein, we summarize the capabilities of various nucleic acid and protein-based detection methods developed for VOCs in identifying and differentiating current VOCs and compare the advantages and disadvantages of each method, providing a basis for the rapid detection of VOCs strains and their future variants and the adoption of corresponding preventive and control measures.

Development of a simple genotyping method based on indel mutations to rapidly screen SARS-CoV-2 circulating variants: Delta, Omicron BA.1 and BA.2

The high need of rapid and flexible tools that facilitate the identification of circulating SARS-CoV-2 Variants of Concern (VOCs) remains crucial for public health system monitoring.

Here, we develop allele-specific (AS)-qPCR assays targeting three recurrent indel mutations, ΔEF156–157, Ins214EPE and ΔLPP24–26, in spike (S) gene to identify the Delta VOC and the Omicron sublineages BA.1 and BA.2, respectively.

After verification of the analytical specificity of each primer set, two duplex qPCR assays with melting curve analysis were performed to screen 129 COVID-19 cases confirmed between December 31, 2021 and February 01, 2022 in Sfax, Tunisia.

The first duplex assay targeting ΔEF156–157 and Ins214EPE mutations successfully detected the Delta VOC in 39 cases and Omicron BA.1 in 83 cases. All the remaining cases (n = 7) were identified as Omicron BA.2, by the second duplex assay targeting Ins214EPE and ΔLPP24–26 mutations. The results of the screening method were in perfect concordance with those of S gene partial sequencing. In conclusion, our findings provide a simple and flexible screening method for more rapid and reliable monitoring of circulating VOCs. We highly recommend its implementation to guide public health policies.